In silico strategies for modeling RNA aptamers and predicting binding sites of their molecular targets

Abstract

RNA aptamers are single-stranded nucleic acids of 20–100 nucleotides, with high sensitivity and specificity against particular molecular targets. In vitro production and selection of aptamers can be performed using the SELEX method. However, this procedure requires considerable time and cost. In this sense, bioinformatics tools play an important role in reducing the time and cost associated with development and production of aptamers. In this article, we propose bioinformatics strategies for modeling and analysis of the interaction with molecular targets for two RNA aptamers: ATP binding RNA aptamer and iSpinach aptamer. For this purpose, molecular modeling of the tertiary structure of the aptamers was performed with two servers (SimRNA and RNAComposer); and AutoDock Vina and rDock programs were used to dock their respective ligands. The predictions developed with these methods could be used for in silico design of RNA aptamers, through a simple and accessible methodology.

Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1951754 .

Keywords:

• RNA aptamer
• RNA modeling
• docking

Disclosure statement

The authors report no conflicts of interest in this work.

Funding

This research was funded by Secretaría de Investigación y Posgrado (IP N) grant numbers 20211520 and 20211631.